Precision editing of microbiome using engineered bacteriophages

Microbial communities exist in complex and highly interconnected networks of interactions that is not fully understood. Advances in “omics” technologies have facilitated the survey of microbiomes under different environments. However, discerning the role of specific members in the community from omics data is difficult. Therefore, we need to develop tools precisely edit the composition of a microbial community in situ. Precision tools to edit a microbiome will enable a quantitative understanding of how interactions of individual microbes shape community structure, stability and response to perturbations. Current approaches to modifying the composition of a microbiome in situ (antibiotics, mobile DNA, nutrition and microbiota transplant) lack the precision necessary for species-specific editing. We are developing tools to design a panel of obligate lytic phages to precisely edit a microbial community by eliminating specific microbial species. This approach can be modified to deliver genetic payloads to specific members within a community.